github-actions[bot]
commented
1 week ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 0 |
| Error | 1 |
| Failure | 0 |
| Skipped | 0 |
Errored Tests
*❌ WGS-PE-variant-calling-in-haploid-system.ga_0
**Execution Problem:**
* ```
Failed to run workflow, at least one job is in [error] state.
```
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: Paired Collection**: * step_state: scheduled - **Step 2: Annotation GTF**: * step_state: scheduled - **Step 11: toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_viterbi/lofreq\_viterbi/2.1.5+galaxy0**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq viterbi --ref 'reference.fa' --defqual 2 --out tmp.bam '/tmp/tmprsgjhw6k/files/4/1/4/dataset_414cf091-fae9-4c6a-bd70-e5e128f751e7.dat' && samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmprsgjhw6k/job_working_directory/000/20/outputs/dataset_a23283d2-66a5-4346-b41a-6fe604d49140.dat' tmp.bam ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` | | adv\_options | ` {"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false} ` | | chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"} ` | - **Job 2:** * Job state is ok **Command Line:** * ```console ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq viterbi --ref 'reference.fa' --defqual 2 --out tmp.bam '/tmp/tmprsgjhw6k/files/3/9/f/dataset_39fcddb1-619b-418c-aa8e-8a1756f41fb4.dat' && samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmprsgjhw6k/job_working_directory/000/21/outputs/dataset_4addbe06-522b-43ae-8624-f5b59c083199.dat' tmp.bam ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` | | adv\_options | ` {"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false} ` | | chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"} ` | - **Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_call/lofreq\_call/2.1.5+galaxy3**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/tmp/tmprsgjhw6k/files/a/2/3/dataset_a23283d2-66a5-4346-b41a-6fe604d49140.dat' reads.bam && ln -s -f '/tmp/tmprsgjhw6k/files/_metadata_files/5/3/2/metadata_532e6e30-686a-416b-8008-01030c7a13e1.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
INFO [2024-11-04 05:23:28,346]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam
INFO [2024-11-04 05:23:28,374]: Adding 19 commands to mp-pool
Checking the headers and starting positions of 19 files
Number of substitution tests performed: 189
Number of indel tests performed: 21
INFO [2024-11-04 05:23:32,058]: Executing lofreq filter -i /tmp/tmprsgjhw6k/tmp/lofreq2_call_parallel_6ah89gq/concat.vcf.gz -o variants.vcf --snvqual-thresh 43 --indelqual-thresh 33
set_lofreq_standard
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| call\_control | ` {"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "20", "min_bq": "20"}, "coverage": {"max_depth": "1000000", "min_cov": "10"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_control | ` {"__current_case__": 2, "bonf": "dynamic", "filter_type": "set_lofreq_standard", "others": "", "sig": "0.01"} ` |
| reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"} ` |
| regions | ` {"__current_case__": 0, "restrict_to_region": "genome"} ` |
| variant\_types | ` "--call-indels" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/tmp/tmprsgjhw6k/files/4/a/d/dataset_4addbe06-522b-43ae-8624-f5b59c083199.dat' reads.bam && ln -s -f '/tmp/tmprsgjhw6k/files/_metadata_files/a/2/5/metadata_a2596e11-673c-47d0-81ef-99015af089a4.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
INFO [2024-11-04 05:23:28,342]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam
INFO [2024-11-04 05:23:28,372]: Adding 19 commands to mp-pool
Checking the headers and starting positions of 19 files
Number of substitution tests performed: 189
Number of indel tests performed: 20
INFO [2024-11-04 05:23:32,237]: Executing lofreq filter -i /tmp/tmprsgjhw6k/tmp/lofreq2_call_parallellxshxa5k/concat.vcf.gz -o variants.vcf --snvqual-thresh 43 --indelqual-thresh 33
set_lofreq_standard
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| call\_control | ` {"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "20", "min_bq": "20"}, "coverage": {"max_depth": "1000000", "min_cov": "10"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_control | ` {"__current_case__": 2, "bonf": "dynamic", "filter_type": "set_lofreq_standard", "others": "", "sig": "0.01"} ` |
| reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"} ` |
| regions | ` {"__current_case__": 0, "restrict_to_region": "genome"} ` |
| variant\_types | ` "--call-indels" ` |
</details>
- **Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmprsgjhw6k/job_working_directory/000/24/configs/tmpuy09tbmz' '/tmp/tmprsgjhw6k/files/6/e/d/dataset_6edcf9ec-c0dc-48b0-9a35-fae64b8f1806.dat' > '/tmp/tmprsgjhw6k/job_working_directory/000/24/outputs/dataset_9194ee81-fd89-4f43-835d-6382959a4ba8.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "/^#/ { print; next } ($4 ~ /^[ACGT]$/ && $5 ~ /^[ACGT]$/) { print }" ` |
| dbkey | ` "?" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmprsgjhw6k/job_working_directory/000/25/configs/tmpgb4n6s_7' '/tmp/tmprsgjhw6k/files/0/8/b/dataset_08bc1284-9ad7-41ef-b0f8-38a44d94b922.dat' > '/tmp/tmprsgjhw6k/job_working_directory/000/25/outputs/dataset_0aef1599-8d00-46b4-b279-c0c11d1eb558.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "/^#/ { print; next } ($4 ~ /^[ACGT]$/ && $5 ~ /^[ACGT]$/) { print }" ` |
| dbkey | ` "?" ` |
</details>
- **Step 14: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is error
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| annotations | ` ["-formatEff", "-classic"] ` |
| chr | ` "" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| csvStats | ` false ` |
| dbkey | ` "?" ` |
| filter | ` {"__current_case__": 0, "specificEffects": "no"} ` |
| filterOut | ` ["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"] ` |
| generate\_stats | ` true ` |
| inputFormat | ` "vcf" ` |
| intervals | ` None ` |
| noLog | ` true ` |
| offset | ` "default" ` |
| outputConditional | ` {"__current_case__": 0, "outputFormat": "vcf"} ` |
| outputFormat | ` "vcf" ` |
| snpDb | ` {"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 15, "src": "hda"}]}} ` |
| spliceRegion | ` {"__current_case__": 0, "setSpliceRegions": "no"} ` |
| spliceSiteSize | ` None ` |
| transcripts | ` None ` |
| udLength | ` "0" ` |
- **Job 2:**
* Job state is error
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| annotations | ` ["-formatEff", "-classic"] ` |
| chr | ` "" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| csvStats | ` false ` |
| dbkey | ` "?" ` |
| filter | ` {"__current_case__": 0, "specificEffects": "no"} ` |
| filterOut | ` ["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"] ` |
| generate\_stats | ` true ` |
| inputFormat | ` "vcf" ` |
| intervals | ` None ` |
| noLog | ` true ` |
| offset | ` "default" ` |
| outputConditional | ` {"__current_case__": 0, "outputFormat": "vcf"} ` |
| outputFormat | ` "vcf" ` |
| snpDb | ` {"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 15, "src": "hda"}]}} ` |
| spliceRegion | ` {"__current_case__": 0, "setSpliceRegions": "no"} ` |
| spliceSiteSize | ` None ` |
| transcripts | ` None ` |
| udLength | ` "0" ` |
</details>
- **Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift\_extractFields/4.3+t.galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "vcf" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| empty\_text | ` "." ` |
| extract | ` "CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID" ` |
| one\_effect\_per\_line | ` true ` |
| separator | ` "" ` |
- **Job 2:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "vcf" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| empty\_text | ` "." ` |
| extract | ` "CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID" ` |
| one\_effect\_per\_line | ` true ` |
| separator | ` "" ` |
</details>
- **Step 16: toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filename | ` {"__current_case__": 0, "add_name": true, "place_name": "same_multiple"} ` |
| one\_header | ` true ` |
</details>
- **Step 3: Genome fasta**:
* step_state: scheduled
- **Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -sf '/tmp/tmprsgjhw6k/files/8/2/5/dataset_8250b76f-78c8-4834-accb-30c5d5747bc6.dat' 'ERR018930.fastqsanger.gz' && ln -sf '/tmp/tmprsgjhw6k/files/8/d/3/dataset_8d3f8427-6300-4aa9-aa20-deb1ab128523.dat' 'ERR018930_R2.fastqsanger.gz' && cp '/tmp/tmprsgjhw6k/job_working_directory/000/7/configs/tmp6s_591_1' galaxy.json && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR018930.fastqsanger.gz' -i 'ERR018930.fastqsanger.gz' -I 'ERR018930_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz && mv first.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/7/outputs/dataset_09699904-aedd-4004-9aeb-6bf22d2296e2.dat' && mv second.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/7/outputs/dataset_1984aff0-89ca-4528-abdd-205d9eee3f03.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Read1 before filtering:
total reads: 7337
total bases: 555502
Q20 bases: 496161(89.3176%)
Q30 bases: 321585(57.8909%)
Read2 before filtering:
total reads: 7337
total bases: 555512
Q20 bases: 501389(90.2571%)
Q30 bases: 309357(55.6886%)
Read1 after filtering:
total reads: 7337
total bases: 555502
Q20 bases: 496161(89.3176%)
Q30 bases: 321585(57.8909%)
Read2 after filtering:
total reads: 7337
total bases: 555512
Q20 bases: 501389(90.2571%)
Q30 bases: 309357(55.6886%)
Filtering result:
reads passed filter: 14674
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0
Duplication rate: 0.0408886%
Insert size peak (evaluated by paired-end reads): 108
JSON report: fastp.json
HTML report: fastp.html
fastp --thread 1 --report_title fastp report for ERR018930.fastqsanger.gz -i ERR018930.fastqsanger.gz -I ERR018930_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz
fastp v0.23.4, time used: 1 seconds
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_options | ` {"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}} ` |
| output\_options | ` {"report_html": true, "report_json": true} ` |
| overrepresented\_sequence\_analysis | ` {"overrepresentation_analysis": false, "overrepresentation_sampling": null} ` |
| read\_mod\_options | ` {"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}} ` |
| single\_paired | ` {"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"} ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
ln -sf '/tmp/tmprsgjhw6k/files/5/3/b/dataset_53be5bb6-10ae-46d7-a9b4-bebe9e7a6ac2.dat' 'ERR1035492.fastqsanger.gz' && ln -sf '/tmp/tmprsgjhw6k/files/a/8/e/dataset_a8e85b43-d213-441a-a5dc-acdc1ea5df54.dat' 'ERR1035492_R2.fastqsanger.gz' && cp '/tmp/tmprsgjhw6k/job_working_directory/000/8/configs/tmpdkopod5b' galaxy.json && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR1035492.fastqsanger.gz' -i 'ERR1035492.fastqsanger.gz' -I 'ERR1035492_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz && mv first.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/8/outputs/dataset_f8f18331-4568-4a28-9b70-354a4e4a2bc0.dat' && mv second.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/8/outputs/dataset_a3b64c44-3692-4a26-9f59-e48022458c52.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Read1 before filtering:
total reads: 6031
total bases: 602346
Q20 bases: 585185(97.151%)
Q30 bases: 549984(91.307%)
Read2 before filtering:
total reads: 6031
total bases: 602346
Q20 bases: 576449(95.7006%)
Q30 bases: 529319(87.8762%)
Read1 after filtering:
total reads: 6031
total bases: 602346
Q20 bases: 585185(97.151%)
Q30 bases: 549984(91.307%)
Read2 after filtering:
total reads: 6031
total bases: 602346
Q20 bases: 576449(95.7006%)
Q30 bases: 529319(87.8762%)
Filtering result:
reads passed filter: 12062
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0
Duplication rate: 0.381363%
Insert size peak (evaluated by paired-end reads): 165
JSON report: fastp.json
HTML report: fastp.html
fastp --thread 1 --report_title fastp report for ERR1035492.fastqsanger.gz -i ERR1035492.fastqsanger.gz -I ERR1035492_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz
fastp v0.23.4, time used: 1 seconds
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_options | ` {"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}} ` |
| output\_options | ` {"report_html": true, "report_json": true} ` |
| overrepresented\_sequence\_analysis | ` {"overrepresentation_analysis": false, "overrepresentation_sampling": null} ` |
| read\_mod\_options | ` {"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}} ` |
| single\_paired | ` {"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 4, "src": "dce"}]}, "single_paired_selector": "paired_collection"} ` |
</details>
- **Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff\_build\_gb/5.2+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
mkdir -p '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files/snpeff_db' && mkdir -p snpeff_output/'snpeff_db' && ln -s '/tmp/tmprsgjhw6k/files/8/7/f/dataset_87f491bf-e94b-481e-8bfd-bba8dc4681d2.dat' 'snpeff_output/snpeff_db/sequences.fa.gz' && ln -s '/tmp/tmprsgjhw6k/files/6/0/5/dataset_6055fbce-5604-4838-8b19-b422f8c5cd19.dat' 'snpeff_output/snpeff_db/genes.gtf' && snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m build -noCheckCds -noCheckProtein -v -configOption 'snpeff_db'.genome='snpeff_db' -configOption 'snpeff_db'.codonTable='Standard' -gtf22 -dataDir "$(pwd)/snpeff_output" 'snpeff_db' && mv snpeff_output/'snpeff_db'/*.bin '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files/snpeff_db' && echo 'snpeff_db.genome : snpeff_db' >> '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files'/snpEff.config && echo 'snpeff_db.codonTable : Standard' >> '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files'/snpEff.config
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'snpeff_db'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'snpeff_db'
00:00:00 Reading config file: /tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'snpeff_db'
00:00:01 done
00:00:01 Reading GTF22 data file : '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/genes.gtf'
00:00:01 Reading file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/genes.gtf'
....................................................................................................
10000 ....................................................................................................
20000 ..............................................00:00:03
Total: 24693 markers added.
00:00:03 Create exons from CDS (if needed):
00:00:03 Exons created for 1466 transcripts.
00:00:03 Deleting redundant exons (if needed):
.
0 ............................................00:00:03 Total transcripts with deleted exons: 4424
00:00:03 Collapsing zero length introns (if needed):
00:00:04 Total collapsed transcripts: 0
00:00:04 Reading sequences :
00:00:04 FASTA file: '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/genomes/snpeff_db.fa' not found.
00:00:04 Reading FASTA file: '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequences.fa'
00:00:04 Reading sequence 'NC_009906.1', length: 830022
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (174 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (381 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009907.1', length: 755035
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (158 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (394 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009908.2', length: 1011127
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (218 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (578 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009909.1', length: 876622
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (203 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (548 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009910.1', length: 1370936
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (312 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (806 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009911.1', length: 1033388
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (241 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (634 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009912.1', length: 1497819
00:00:04 Adding genomic sequences to genes:
00:00:04 Done (343 sequences added).
00:00:04 Adding genomic sequences to exons:
00:00:04 Done (901 sequences added, 0 ignored).
00:00:04 Reading sequence 'NC_009913.1', length: 1678596
00:00:04 Adding genomic sequences to genes:
00:00:05 Done (368 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (945 sequences added, 0 ignored).
00:00:05 Reading sequence 'NC_009914.1', length: 1923364
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (430 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (1173 sequences added, 0 ignored).
00:00:05 Reading sequence 'NC_009915.1', length: 1419739
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (317 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (753 sequences added, 0 ignored).
00:00:05 Reading sequence 'NC_009916.1', length: 2067354
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (444 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (1225 sequences added, 0 ignored).
00:00:05 Reading sequence 'NC_009917.1', length: 3004884
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (676 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (1795 sequences added, 0 ignored).
00:00:05 Reading sequence 'NC_009918.1', length: 2031768
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (442 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (1178 sequences added, 0 ignored).
00:00:05 Reading sequence 'NC_009919.1', length: 3120417
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (682 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (1662 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852640.1', length: 1000
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852639.1', length: 995
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852638.1', length: 877
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852637.1', length: 585
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852636.1', length: 1026
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852635.1', length: 900
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852634.1', length: 759
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852633.1', length: 1551
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852632.1', length: 563
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852631.1', length: 748
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852630.1', length: 1037
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852629.1', length: 416
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852628.1', length: 769
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852627.1', length: 1184
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852626.1', length: 900
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852625.1', length: 1255
00:00:05 Adding genomic sequences to genes:
00:00:05 Done (0 sequences added).
00:00:05 Adding genomic sequences to exons:
00:00:05 Done (0 sequences added, 0 ignored).
00:00:05 Reading sequence 'NW_001852624.1', length: 1294
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852623.1', length: 927
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852622.1', length: 664
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852621.1', length: 883
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852620.1', length: 1143
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852619.1', length: 652
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852618.1', length: 1396
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852617.1', length: 2007
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852616.1', length: 648
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852615.1', length: 2179
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852614.1', length: 786
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852613.1', length: 736
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852612.1', length: 1033
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852611.1', length: 2123
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852610.1', length: 3939
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852609.1', length: 1375
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (1 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (2 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852608.1', length: 1001
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852607.1', length: 908
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852606.1', length: 1938
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852605.1', length: 879
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852604.1', length: 3240
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852603.1', length: 803
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852602.1', length: 535
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852601.1', length: 1041
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852600.1', length: 877
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852599.1', length: 1281
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852598.1', length: 1004
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852597.1', length: 992
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852596.1', length: 1431
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852595.1', length: 1034
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852594.1', length: 785
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852593.1', length: 936
00:00:06 Adding genomic sequences to genes:
00:00:06 Done (0 sequences added).
00:00:06 Adding genomic sequences to exons:
00:00:06 Done (0 sequences added, 0 ignored).
00:00:06 Reading sequence 'NW_001852592.1', length: 952
00:00:06 Adding genomic sequences to genes:
..
d
# 'NW_001851052.1' 723 Standard
# 'NW_001851247.1' 723 Standard
# 'NW_001850604.1' 722 Standard
# 'NW_001851896.1' 722 Standard
# 'NW_001852533.1' 722 Standard
# 'NW_001850697.1' 721 Standard
# 'NW_001852332.1' 721 Standard
# 'NW_001850827.1' 720 Standard
# 'NW_001850835.1' 720 Standard
# 'NW_001850932.1' 720 Standard
# 'NW_001851438.1' 720 Standard
# 'NW_001851764.1' 720 Standard
# 'NW_001851031.1' 719 Standard
# 'NW_001851731.1' 719 Standard
# 'NW_001851442.1' 718 Standard
# 'NW_001850386.1' 717 Standard
# 'NW_001852233.1' 717 Standard
# 'NW_001850575.1' 716 Standard
# 'NW_001851005.1' 716 Standard
# 'NW_001850407.1' 715 Standard
# 'NW_001850696.1' 715 Standard
# 'NW_001850996.1' 715 Standard
# 'NW_001850658.1' 714 Standard
# 'NW_001850883.1' 714 Standard
# 'NW_001851045.1' 714 Standard
# 'NW_001851251.1' 714 Standard
# 'NW_001850065.1' 713 Standard
# 'NW_001850479.1' 713 Standard
# 'NW_001850629.1' 713 Standard
# 'NW_001850754.1' 712 Standard
# 'NW_001850759.1' 711 Standard
# 'NW_001850945.1' 711 Standard
# 'NW_001851278.1' 711 Standard
# 'NW_001850412.1' 709 Standard
# 'NW_001851865.1' 709 Standard
# 'NW_001850487.1' 708 Standard
# 'NW_001850480.1' 707 Standard
# 'NW_001850645.1' 705 Standard
# 'NW_001850859.1' 705 Standard
# 'NW_001851893.1' 705 Standard
# 'NW_001850749.1' 704 Standard
# 'NW_001851858.1' 703 Standard
# 'NW_001852190.1' 703 Standard
# 'NW_001850876.1' 702 Standard
# 'NW_001851524.1' 701 Standard
# 'NW_001850359.1' 700 Standard
# 'NW_001850753.1' 700 Standard
# 'NW_001851060.1' 700 Standard
# 'NW_001851908.1' 700 Standard
# 'NW_001850450.1' 699 Standard
# 'NW_001850602.1' 699 Standard
# 'NW_001851328.1' 698 Standard
# 'NW_001852308.1' 698 Standard
# 'NW_001851545.1' 696 Standard
# 'NW_001850699.1' 695 Standard
# 'NW_001851015.1' 695 Standard
# 'NW_001852340.1' 695 Standard
# 'NW_001850418.1' 693 Standard
# 'NW_001850686.1' 693 Standard
# 'NW_001850989.1' 693 Standard
# 'NW_001851933.1' 693 Standard
# 'NW_001851946.1' 693 Standard
# 'NW_001852141.1' 693 Standard
# 'NW_001850504.1' 692 Standard
# 'NW_001850632.1' 692 Standard
# 'NW_001852009.1' 692 Standard
# 'NW_001852071.1' 692 Standard
# 'NW_001850349.1' 691 Standard
# 'NW_001850825.1' 691 Standard
# 'NW_001851785.1' 691 Standard
# 'NW_001850649.1' 690 Standard
# 'NW_001851121.1' 690 Standard
# 'NW_001852499.1' 690 Standard
# 'NW_001850411.1' 688 Standard
# 'NW_001850533.1' 688 Standard
# 'NW_001852537.1' 687 Standard
# 'NW_001850096.1' 686 Standard
# 'NW_001850957.1' 686 Standard
# 'NW_001852305.1' 686 Standard
# 'NW_001850460.1' 685 Standard
# 'NW_001851222.1' 685 Standard
# 'NW_001851940.1' 685 Standard
# 'NW_001850334.1' 684 Standard
# 'NW_001850454.1' 684 Standard
# 'NW_001850942.1' 684 Standard
# 'NW_001850374.1' 682 Standard
# 'NW_001850492.1' 681 Standard
# 'NW_001850494.1' 681 Standard
# 'NW_001850975.1' 681 Standard
# 'NW_001850398.1' 680 Standard
# 'NW_001851640.1' 679 Standard
# 'NW_001852294.1' 679 Standard
# 'NW_001851769.1' 678 Standard
# 'NW_001850338.1' 677 Standard
# 'NW_001850419.1' 677 Standard
# 'NW_001851887.1' 677 Standard
# 'NW_001850100.1' 676 Standard
# 'NW_001850512.1' 676 Standard
# 'NW_001851745.1' 676 Standard
# 'NW_001850524.1' 675 Standard
# 'NW_001851245.1' 673 Standard
# 'NW_001852350.1' 673 Standard
# 'NW_001850586.1' 672 Standard
# 'NW_001850776.1' 672 Standard
# 'NW_001852395.1' 672 Standard
# 'NW_001851038.1' 671 Standard
# 'NW_001850867.1' 670 Standard
# 'NW_001851275.1' 670 Standard
# 'NW_001851936.1' 670 Standard
# 'NW_001850718.1' 668 Standard
# 'NW_001850862.1' 668 Standard
# 'NW_001851172.1' 668 Standard
# 'NW_001852353.1' 668 Standard
# 'NW_001850375.1' 667 Standard
# 'NW_001850636.1' 667 Standard
# 'NW_001852182.1' 667 Standard
# 'NW_001852426.1' 667 Standard
# 'NW_001850433.1' 664 Standard
# 'NW_001852622.1' 664 Standard
# 'NW_001850067.1' 663 Standard
# 'NW_001850491.1' 663 Standard
# 'NW_001849929.1' 661 Standard
# 'NW_001850748.1' 660 Standard
# 'NW_001851017.1' 660 Standard
# 'NW_001851932.1' 660 Standard
# 'NW_001850514.1' 658 Standard
# 'NW_001851679.1' 658 Standard
# 'NW_001851715.1' 656 Standard
# 'NW_001849982.1' 655 Standard
# 'NW_001852377.1' 655 Standard
# 'NW_001851939.1' 654 Standard
# 'NW_001852173.1' 654 Standard
# 'NW_001851501.1' 653 Standard
# 'NW_001852619.1' 652 Standard
# 'NW_001850901.1' 651 Standard
# 'NW_001850757.1' 648 Standard
# 'NW_001852616.1' 648 Standard
# 'NW_001850101.1' 646 Standard
# 'NW_001850875.1' 646 Standard
# 'NW_001852161.1' 645 Standard
# 'NW_001852025.1' 644 Standard
# 'NW_001851266.1' 643 Standard
# 'NW_001850370.1' 641 Standard
# 'NW_001852379.1' 640 Standard
# 'NW_001851298.1' 639 Standard
# 'NW_001851657.1' 639 Standard
# 'NW_001850455.1' 638 Standard
# 'NW_001852145.1' 638 Standard
# 'NW_001850477.1' 636 Standard
# 'NW_001850400.1' 634 Standard
# 'NW_001850443.1' 634 Standard
# 'NW_001850515.1' 633 Standard
# 'NW_001851387.1' 632 Standard
# 'NW_001851851.1' 632 Standard
# 'NW_001850560.1' 630 Standard
# 'NW_001850761.1' 630 Standard
# 'NW_001850368.1' 629 Standard
# 'NW_001851888.1' 629 Standard
# 'NW_001852297.1' 629 Standard
# 'NW_001850500.1' 628 Standard
# 'NW_001850499.1' 626 Standard
# 'NW_001850908.1' 626 Standard
# 'NW_001850371.1' 625 Standard
# 'NW_001850986.1' 625 Standard
# 'NW_001850336.1' 624 Standard
# 'NW_001850687.1' 624 Standard
# 'NW_001852365.1' 624 Standard
# 'NW_001852266.1' 623 Standard
# 'NW_001852378.1' 621 Standard
# 'NW_001850518.1' 620 Standard
# 'NW_001850849.1' 620 Standard
# 'NW_001851945.1' 620 Standard
# 'NW_001851891.1' 619 Standard
# 'NW_001851458.1' 618 Standard
# 'NW_001850830.1' 615 Standard
# 'NW_001850935.1' 614 Standard
# 'NW_001852111.1' 614 Standard
# 'NW_001850506.1' 613 Standard
# 'NW_001850674.1' 612 Standard
# 'NW_001850725.1' 609 Standard
# 'NW_001850501.1' 608 Standard
# 'NW_001850800.1' 606 Standard
# 'NW_001850874.1' 606 Standard
# 'NW_001851789.1' 603 Standard
# 'NW_001852326.1' 603 Standard
# 'NW_001851294.1' 601 Standard
# 'NW_001851186.1' 598 Standard
# 'NW_001851832.1' 598 Standard
# 'NW_001852296.1' 597 Standard
# 'NW_001850824.1' 594 Standard
# 'NW_001851830.1' 594 Standard
# 'NW_001851753.1' 593 Standard
# 'NW_001850000.1' 592 Standard
# 'NW_001850498.1' 590 Standard
# 'NW_001851290.1' 587 Standard
# 'NW_001851090.1' 585 Standard
# 'NW_001852637.1' 585 Standard
# 'NW_001850643.1' 583 Standard
# 'NW_001850401.1' 582 Standard
# 'NW_001850594.1' 582 Standard
# 'NW_001852116.1' 581 Standard
# 'NW_001850554.1' 579 Standard
# 'NW_001851024.1' 579 Standard
# 'NW_001850816.1' 578 Standard
# 'NW_001850822.1' 576 Standard
# 'NW_001850509.1' 575 Standard
# 'NW_001850635.1' 575 Standard
# 'NW_001850929.1' 575 Standard
# 'NW_001850369.1' 574 Standard
# 'NW_001850493.1' 574 Standard
# 'NW_001850395.1' 571 Standard
# 'NW_001851505.1' 570 Standard
# 'NW_001851631.1' 570 Standard
# 'NW_001850713.1' 565 Standard
# 'NW_001851809.1' 564 Standard
# 'NW_001850061.1' 563 Standard
# 'NW_001852632.1' 563 Standard
# 'NW_001851161.1' 562 Standard
# 'NW_001850765.1' 559 Standard
# 'NW_001850895.1' 558 Standard
# 'NW_001850978.1' 557 Standard
# 'NW_001850431.1' 551 Standard
# 'NW_001850709.1' 551 Standard
# 'NW_001850611.1' 550 Standard
# 'NW_001851035.1' 544 Standard
# 'NW_001850364.1' 543 Standard
# 'NW_001850701.1' 543 Standard
# 'NW_001850855.1' 539 Standard
# 'NW_001850597.1' 535 Standard
# 'NW_001852602.1' 535 Standard
# 'NW_001850655.1' 533 Standard
# 'NW_001852156.1' 531 Standard
# 'NW_001852269.1' 531 Standard
# 'NW_001850857.1' 529 Standard
# 'NW_001850333.1' 528 Standard
# 'NW_001850777.1' 526 Standard
# 'NW_001851162.1' 525 Standard
# 'NW_001851082.1' 522 Standard
# 'NW_001852486.1' 522 Standard
# 'NW_001852281.1' 521 Standard
# 'NW_001850666.1' 520 Standard
# 'NW_001850967.1' 518 Standard
# 'NW_001851126.1' 516 Standard
# 'NW_001850940.1' 515 Standard
# 'NW_001850796.1' 510 Standard
# 'NW_001850770.1' 508 Standard
# 'NW_001850871.1' 506 Standard
# 'NW_001851101.1' 495 Standard
# 'NW_001850814.1' 493 Standard
# 'NW_001850789.1' 491 Standard
# 'NW_001850928.1' 491 Standard
# 'NW_001850601.1' 488 Standard
# 'NW_001850841.1' 488 Standard
# 'NW_001850682.1' 485 Standard
# 'NW_001850663.1' 482 Standard
# 'NW_001852030.1' 480 Standard
# 'NW_001850376.1' 478 Standard
# 'NW_001850730.1' 478 Standard
# 'NW_001850614.1' 477 Standard
# 'NW_001850468.1' 475 Standard
# 'NW_001851859.1' 471 Standard
# 'NW_001851435.1' 468 Standard
# 'NW_001851845.1' 463 Standard
# 'NW_001850609.1' 461 Standard
# 'NW_001851377.1' 458 Standard
# 'NW_001850771.1' 456 Standard
# 'NW_001851274.1' 456 Standard
# 'NW_001850894.1' 455 Standard
# 'NW_001852355.1' 455 Standard
# 'NW_001852529.1' 454 Standard
# 'NW_001852035.1' 451 Standard
# 'NW_001850745.1' 447 Standard
# 'NW_001851895.1' 446 Standard
# 'NW_001852246.1' 446 Standard
# 'NW_001850952.1' 445 Standard
# 'NW_001850330.1' 441 Standard
# 'NW_001850705.1' 440 Standard
# 'NW_001850097.1' 438 Standard
# 'NW_001850537.1' 428 Standard
# 'NW_001850766.1' 428 Standard
# 'NW_001850406.1' 427 Standard
# 'NW_001850094.1' 426 Standard
# 'NW_001852530.1' 424 Standard
# 'NW_001850608.1' 419 Standard
# 'NW_001851375.1' 419 Standard
# 'NW_001851154.1' 417 Standard
# 'NW_001852055.1' 416 Standard
# 'NW_001852629.1' 416 Standard
# 'NW_001850671.1' 415 Standard
# 'NW_001852047.1' 412 Standard
# 'NW_001852202.1' 412 Standard
# 'NW_001852390.1' 411 Standard
# 'NW_001850898.1' 409 Standard
# 'NW_001850979.1' 409 Standard
# 'NW_001850920.1' 406 Standard
# 'NW_001850768.1' 403 Standard
# 'NW_001850782.1' 403 Standard
# 'NW_001850839.1' 401 Standard
# 'NW_001850783.1' 400 Standard
# 'NW_001850731.1' 398 Standard
# 'NW_001851261.1' 396 Standard
# 'NW_001850517.1' 393 Standard
# 'NW_001850931.1' 393 Standard
# 'NW_001850907.1' 390 Standard
# 'NW_001852391.1' 387 Standard
# 'NW_001850740.1' 386 Standard
# 'NW_001850956.1' 385 Standard
# 'NW_001850742.1' 384 Standard
# 'NW_001852125.1' 384 Standard
# 'NW_001850870.1' 382 Standard
# 'NW_001851899.1' 382 Standard
# 'NW_001850872.1' 380 Standard
# 'NW_001850739.1' 378 Standard
# 'NW_001851953.1' 378 Standard
# 'NW_001850598.1' 376 Standard
# 'NW_001851206.1' 376 Standard
# 'NW_001850831.1' 375 Standard
# 'NW_001850606.1' 374 Standard
# 'NW_001850747.1' 373 Standard
# 'NW_001850798.1' 372 Standard
# 'NW_001851053.1' 371 Standard
# 'NW_001850662.1' 370 Standard
# 'NW_001850969.1' 368 Standard
# 'NW_001850779.1' 367 Standard
# 'NW_001850919.1' 367 Standard
# 'NW_001850792.1' 366 Standard
# 'NW_001851975.1' 365 Standard
# 'NW_001850906.1' 364 Standard
# 'NW_001850853.1' 360 Standard
# 'NW_001850845.1' 359 Standard
# 'NW_001850780.1' 357 Standard
# 'NW_001852109.1' 356 Standard
# 'NW_001850954.1' 352 Standard
# 'NW_001852431.1' 352 Standard
# 'NW_001850772.1' 350 Standard
# 'NW_001851165.1' 350 Standard
# 'NW_001850600.1' 348 Standard
# 'NW_001850767.1' 347 Standard
# 'NW_001850923.1' 346 Standard
# 'NW_001850391.1' 344 Standard
# 'NW_001851284.1' 340 Standard
# 'NW_001851394.1' 338 Standard
# 'NW_001850781.1' 337 Standard
# 'NW_001851768.1' 337 Standard
# 'NW_001850763.1' 335 Standard
# 'NW_001850961.1' 332 Standard
# 'NW_001851861.1' 326 Standard
# 'NW_001851062.1' 318 Standard
# 'NW_001849951.1' 317 Standard
# 'NW_001850619.1' 315 Standard
# 'NW_001850842.1' 315 Standard
# 'NW_001851371.1' 313 Standard
# 'NW_001850860.1' 311 Standard
# 'NW_001850973.1' 311 Standard
# 'NW_001852103.1' 311 Standard
# 'NW_001850647.1' 310 Standard
# 'NW_001850762.1' 309 Standard
# 'NW_001851355.1' 308 Standard
# 'NW_001850850.1' 305 Standard
# 'NW_001851562.1' 305 Standard
# 'NW_001852189.1' 305 Standard
# 'NW_001850573.1' 304 Standard
# 'NW_001851986.1' 302 Standard
# 'NW_001852034.1' 300 Standard
# 'NW_001851255.1' 299 Standard
# 'NW_001850925.1' 297 Standard
# 'NW_001850424.1' 296 Standard
# 'NW_001850769.1' 296 Standard
# 'NW_001852496.1' 294 Standard
# 'NW_001850627.1' 293 Standard
# 'NW_001850795.1' 293 Standard
# 'NW_001851790.1' 292 Standard
# 'NW_001850755.1' 290 Standard
# 'NW_001850764.1' 290 Standard
# 'NW_001850793.1' 289 Standard
# 'NW_001852489.1' 284 Standard
# 'NW_001850735.1' 283 Standard
# 'NW_001851003.1' 283 Standard
# 'NW_001850807.1' 280 Standard
# 'NW_001850637.1' 272 Standard
# 'NW_001850703.1' 269 Standard
# 'NW_001851910.1' 267 Standard
# 'NW_001851178.1' 266 Standard
# 'NW_001850522.1' 265 Standard
# 'NW_001850959.1' 265 Standard
# 'NW_001852249.1' 262 Standard
# 'NW_001850465.1' 261 Standard
# 'NW_001850787.1' 260 Standard
# 'NW_001851429.1' 259 Standard
# 'NW_001850832.1' 255 Standard
# 'NW_001850656.1' 254 Standard
# 'NW_001850716.1' 252 Standard
# 'NW_001852069.1' 252 Standard
# 'NW_001851909.1' 251 Standard
# 'NW_001851999.1' 251 Standard
# 'NW_001850596.1' 250 Standard
# 'NW_001850854.1' 250 Standard
# 'NW_001852157.1' 250 Standard
# 'NW_001850720.1' 248 Standard
# 'NW_001850684.1' 244 Standard
# 'NW_001851920.1' 244 Standard
# 'NW_001851136.1' 243 Standard
# 'NW_001850852.1' 242 Standard
# 'NW_001850829.1' 241 Standard
# 'NW_001851952.1' 235 Standard
# 'NW_001850773.1' 234 Standard
# 'NW_001850823.1' 233 Standard
# 'NW_001851848.1' 233 Standard
# 'NW_001852108.1' 232 Standard
# 'NW_001850916.1' 230 Standard
# 'NW_001851743.1' 228 Standard
# 'NW_001850679.1' 226 Standard
# 'NW_001850971.1' 225 Standard
# 'NW_001851780.1' 225 Standard
# 'NW_001850634.1' 224 Standard
# 'NW_001850621.1' 223 Standard
# 'NW_001851970.1' 223 Standard
# 'NW_001851989.1' 223 Standard
# 'NW_001850702.1' 221 Standard
# 'NW_001852238.1' 221 Standard
# 'NW_001850803.1' 220 Standard
# 'NW_001851796.1' 220 Standard
# 'NW_001851311.1' 218 Standard
# 'NW_001851048.1' 217 Standard
# 'NW_001850977.1' 216 Standard
# 'NW_001850727.1' 215 Standard
# 'NW_001851238.1' 215 Standard
# 'NW_001850926.1' 213 Standard
# 'NW_001850924.1' 209 Standard
# 'NW_001852215.1' 209 Standard
# 'NW_001850861.1' 207 Standard
# 'NW_001851231.1' 200 Standard
# 'NW_001851799.1' 200 Standard
#-----------------------------------------------
00:00:12 Caracterizing exons by splicing (stage 1) :
.............
00:00:12 Caracterizing exons by splicing (stage 2) :
.............00:00:12 done.
00:00:12 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/protein.fa', nothing done.
00:00:12 Saving database
00:00:16 Saving sequences for chromosome 'NC_009914.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009914.1.bin'
00:00:16 Saving sequences for chromosome 'NC_009916.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009916.1.bin'
00:00:16 Saving sequences for chromosome 'NC_009917.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009917.1.bin'
00:00:17 Saving sequences for chromosome 'NC_009918.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009918.1.bin'
00:00:17 Saving sequences for chromosome 'NC_009919.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009919.1.bin'
00:00:17 Saving sequences for small chromosmes to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.bin'
00:00:19 [Optional] Reading regulation elements: GFF
WARNING_FILE_NOT_FOUND: Cannot read optional regulation file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/regulation.gff', nothing done.
00:00:19 [Optional] Reading regulation elements: BED
00:00:19 Cannot find optional regulation dir '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/regulation.bed/', nothing done.
00:00:19 [Optional] Reading motifs: GFF
WARNING_FILE_NOT_FOUND: Cannot open PWMs file /tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/pwms.bin. Nothing done
00:00:19 Done
00:00:19 Done.
```
**Standard Output:**
* ```console
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| codon\_table | ` "Standard" ` |
| dbkey | ` "?" ` |
| genome\_version | ` "snpeff_db" ` |
| input\_type | ` {"__current_case__": 2, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_type_selector": "gtf", "reference_source": {"__current_case__": 1, "input_fasta": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}} ` |
</details>
- **Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa\_mem/0.7.18**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
set -o | grep -q pipefail && set -o pipefail; ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' 'localref.fa' && bwa index 'localref.fa' && bwa mem -t "${GALAXY_SLOTS:-1}" -v 1 -T '30' -h '5' -Y -q -R '@RG\tID:ERR018930\tSM:ERR018930\tPL:ILLUMINA\tLB:ERR018930' 'localref.fa' '/tmp/tmprsgjhw6k/files/0/9/6/dataset_09699904-aedd-4004-9aeb-6bf22d2296e2.dat' '/tmp/tmprsgjhw6k/files/1/9/8/dataset_1984aff0-89ca-4528-abdd-205d9eee3f03.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmprsgjhw6k/job_working_directory/000/11/outputs/dataset_29853fdd-ba77-48b7-a51d-2b8a7e675bad.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
[bwa_index] Pack FASTA... 0.16 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=54027382, availableWord=15801372
[BWTIncConstructFromPacked] 10 iterations done. 26064326 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48149798 characters processed.
[bwt_gen] Finished constructing BWT in 23 iterations.
[bwa_index] 11.76 seconds elapse.
[bwa_index] Update BWT... 0.14 sec
[bwa_index] Pack forward-only FASTA... 0.10 sec
[bwa_index] Construct SA from BWT and Occ... 5.91 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 18.690 sec; CPU: 18.074 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 242, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (33, 468)
[M::mem_pestat] mean and std.dev: (253.94, 65.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 555)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q -R @RG\tID:ERR018930\tSM:ERR018930\tPL:ILLUMINA\tLB:ERR018930 localref.fa /tmp/tmprsgjhw6k/files/0/9/6/dataset_09699904-aedd-4004-9aeb-6bf22d2296e2.dat /tmp/tmprsgjhw6k/files/1/9/8/dataset_1984aff0-89ca-4528-abdd-205d9eee3f03.dat
[main] Real time: 1.141 sec; CPU: 1.099 sec
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| analysis\_type | ` {"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fastq\_input | ` {"__current_case__": 2, "fastq_input1": {"values": [{"id": 7, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""} ` |
| output\_sort | ` "coordinate" ` |
| reference\_source | ` {"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 16, "src": "hda"}]}, "reference_source_selector": "history"} ` |
| rg | ` {"CN": null, "DS": null, "DT": null, "FO": null, "KS": null, "PG": null, "PI": null, "PL": "ILLUMINA", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_lb_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"} ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
set -o | grep -q pipefail && set -o pipefail; ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' 'localref.fa' && bwa index 'localref.fa' && bwa mem -t "${GALAXY_SLOTS:-1}" -v 1 -T '30' -h '5' -Y -q -R '@RG\tID:ERR1035492\tSM:ERR1035492\tPL:ILLUMINA\tLB:ERR1035492' 'localref.fa' '/tmp/tmprsgjhw6k/files/f/8/f/dataset_f8f18331-4568-4a28-9b70-354a4e4a2bc0.dat' '/tmp/tmprsgjhw6k/files/a/3/b/dataset_a3b64c44-3692-4a26-9f59-e48022458c52.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmprsgjhw6k/job_working_directory/000/12/outputs/dataset_de9f1abb-e8ec-4e9b-8531-1d576b3e553e.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
[bwa_index] Pack FASTA... 0.17 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=54027382, availableWord=15801372
[BWTIncConstructFromPacked] 10 iterations done. 26064326 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48149798 characters processed.
[bwt_gen] Finished constructing BWT in 23 iterations.
[bwa_index] 11.71 seconds elapse.
[bwa_index] Update BWT... 0.15 sec
[bwa_index] Pack forward-only FASTA... 0.10 sec
[bwa_index] Construct SA from BWT and Occ... 5.80 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 18.396 sec; CPU: 17.937 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (185, 232, 297)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 521)
[M::mem_pestat] mean and std.dev: (246.23, 81.16)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 633)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q -R @RG\tID:ERR1035492\tSM:ERR1035492\tPL:ILLUMINA\tLB:ERR1035492 localref.fa /tmp/tmprsgjhw6k/files/f/8/f/dataset_f8f18331-4568-4a28-9b70-354a4e4a2bc0.dat /tmp/tmprsgjhw6k/files/a/3/b/dataset_a3b64c44-3692-4a26-9f59-e48022458c52.dat
[main] Real time: 0.945 sec; CPU: 0.928 sec
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| analysis\_type | ` {"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fastq\_input | ` {"__current_case__": 2, "fastq_input1": {"values": [{"id": 8, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""} ` |
| output\_sort | ` "coordinate" ` |
| reference\_source | ` {"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 16, "src": "hda"}]}, "reference_source_selector": "history"} ` |
| rg | ` {"CN": null, "DS": null, "DT": null, "FO": null, "KS": null, "PG": null, "PI": null, "PL": "ILLUMINA", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_lb_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"} ` |
</details>
- **Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools\_view/samtools\_view/1.20+galaxy3**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/tmp/tmprsgjhw6k/files/2/9/8/dataset_29853fdd-ba77-48b7-a51d-2b8a7e675bad.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/b/f/0/metadata_bf01b080-1ec4-4f9d-b9fd-c179bb007ef5.dat' infile.bai && samtools view -@ $addthreads -b -f 3 -F 0 -G 0 -o outfile infile
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode | ` {"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}} ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/tmp/tmprsgjhw6k/files/d/e/9/dataset_de9f1abb-e8ec-4e9b-8531-1d576b3e553e.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/7/3/c/metadata_73ce6f52-c356-447e-959d-a6d443ba0032.dat' infile.bai && samtools view -@ $addthreads -b -f 3 -F 0 -G 0 -o outfile infile
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode | ` {"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}} ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/samtools\_stats/samtools\_stats/2.0.5**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/tmp/tmprsgjhw6k/files/b/1/f/dataset_b1f6b30f-63df-4ae4-85b6-70f842176a71.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/f/1/3/metadata_f13a1cbe-205a-4a1c-9c6a-3aa6f8ba65b3.dat' infile.bai && samtools stats -@ $addthreads infile > '/tmp/tmprsgjhw6k/job_working_directory/000/15/outputs/dataset_5ffd484f-96ba-4c1c-af93-bca99926f7c2.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| cond\_region | ` {"__current_case__": 0, "select_region": "no"} ` |
| cov\_threshold | ` None ` |
| coverage\_cond | ` {"__current_case__": 0, "coverage_select": "no"} ` |
| dbkey | ` "?" ` |
| filter\_by\_flags | ` {"__current_case__": 1, "filter_flags": "nofilter"} ` |
| gc\_depth | ` None ` |
| insert\_size | ` None ` |
| most\_inserts | ` None ` |
| read\_group | ` None ` |
| read\_length | ` None ` |
| remove\_dups | ` false ` |
| remove\_overlaps | ` false ` |
| sparse | ` false ` |
| split\_output\_cond | ` {"__current_case__": 0, "split_output_selector": "no"} ` |
| trim\_quality | ` None ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/tmp/tmprsgjhw6k/files/6/4/6/dataset_6467edee-3a30-4ff4-aad6-ecd6c02da19b.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/8/3/e/metadata_83e07677-0d79-4441-891b-8b6d7d840f4e.dat' infile.bai && samtools stats -@ $addthreads infile > '/tmp/tmprsgjhw6k/job_working_directory/000/16/outputs/dataset_00151697-aa08-45dc-a945-a8930f87a869.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| cond\_region | ` {"__current_case__": 0, "select_region": "no"} ` |
| cov\_threshold | ` None ` |
| coverage\_cond | ` {"__current_case__": 0, "coverage_select": "no"} ` |
| dbkey | ` "?" ` |
| filter\_by\_flags | ` {"__current_case__": 1, "filter_flags": "nofilter"} ` |
| gc\_depth | ` None ` |
| insert\_size | ` None ` |
| most\_inserts | ` None ` |
| read\_group | ` None ` |
| read\_length | ` None ` |
| remove\_dups | ` false ` |
| remove\_overlaps | ` false ` |
| sparse | ` false ` |
| split\_output\_cond | ` {"__current_case__": 0, "split_output_selector": "no"} ` |
| trim\_quality | ` None ` |
</details>
- **Step 9: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard\_MarkDuplicates/3.1.1.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS && ln -sf '/tmp/tmprsgjhw6k/files/b/1/f/dataset_b1f6b30f-63df-4ae4-85b6-70f842176a71.dat' 'ERR018930' && picard MarkDuplicates --INPUT 'ERR018930' --OUTPUT '/tmp/tmprsgjhw6k/job_working_directory/000/17/outputs/dataset_414cf091-fae9-4c6a-bd70-e5e128f751e7.dat' --METRICS_FILE '/tmp/tmprsgjhw6k/job_working_directory/000/17/outputs/dataset_3616d219-d8fa-4153-aa5c-498ea936e5d1.dat' --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true' --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100' --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmprsgjhw6k/tmp
Nov 04, 2024 5:23:01 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| assume\_sorted | ` true ` |
| barcode\_tag | ` "" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comments | ` [] ` |
| dbkey | ` "?" ` |
| duplicate\_scoring\_strategy | ` "SUM_OF_BASE_QUALITIES" ` |
| optical\_duplicate\_pixel\_distance | ` "100" ` |
| read\_name\_regex | ` "" ` |
| remove\_duplicates | ` true ` |
| validation\_stringency | ` "LENIENT" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS && ln -sf '/tmp/tmprsgjhw6k/files/6/4/6/dataset_6467edee-3a30-4ff4-aad6-ecd6c02da19b.dat' 'ERR1035492' && picard MarkDuplicates --INPUT 'ERR1035492' --OUTPUT '/tmp/tmprsgjhw6k/job_working_directory/000/18/outputs/dataset_39fcddb1-619b-418c-aa8e-8a1756f41fb4.dat' --METRICS_FILE '/tmp/tmprsgjhw6k/job_working_directory/000/18/outputs/dataset_04c86bd6-57cc-4204-b620-2cf2e68dd790.dat' --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true' --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100' --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmprsgjhw6k/tmp
Nov 04, 2024 5:23:01 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| assume\_sorted | ` true ` |
| barcode\_tag | ` "" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comments | ` [] ` |
| dbkey | ` "?" ` |
| duplicate\_scoring\_strategy | ` "SUM_OF_BASE_QUALITIES" ` |
| optical\_duplicate\_pixel\_distance | ` "100" ` |
| read\_name\_regex | ` "" ` |
| remove\_duplicates | ` true ` |
| validation\_stringency | ` "LENIENT" ` |
</details>
- **Step 10: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is running
**Command Line:**
* ```console
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastp_0 && ln -s '/tmp/tmprsgjhw6k/files/3/c/7/dataset_3c7835f2-2669-44ab-a34a-819e7863c5df.dat' 'multiqc_WDir/fastp_0/ERR018930fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR018930fastp.json' || die "'report_title' or 'report_title' not found in the file" && ln -s '/tmp/tmprsgjhw6k/files/e/b/5/dataset_eb59d284-024a-4a6f-827f-31d8f8f38191.dat' 'multiqc_WDir/fastp_0/ERR1035492fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR1035492fastp.json' || die "'report_title' or 'report_title' not found in the file" && mkdir multiqc_WDir/samtools_1 && mkdir 'multiqc_WDir/samtools_1/stats_0' && grep -q 'This file was produced by samtools stats' /tmp/tmprsgjhw6k/files/5/f/f/dataset_5ffd484f-96ba-4c1c-af93-bca99926f7c2.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR018930'" && ln -s '/tmp/tmprsgjhw6k/files/5/f/f/dataset_5ffd484f-96ba-4c1c-af93-bca99926f7c2.dat' 'multiqc_WDir/samtools_1/stats_0/ERR018930' && grep -q 'This file was produced by samtools stats' /tmp/tmprsgjhw6k/files/0/0/1/dataset_00151697-aa08-45dc-a945-a8930f87a869.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR1035492'" && ln -s '/tmp/tmprsgjhw6k/files/0/0/1/dataset_00151697-aa08-45dc-a945-a8930f87a869.dat' 'multiqc_WDir/samtools_1/stats_0/ERR1035492' && mkdir multiqc_WDir/picard_2 && mkdir 'multiqc_WDir/picard_2/markdups_0' && grep -q 'MarkDuplicates' /tmp/tmprsgjhw6k/files/3/6/1/dataset_3616d219-d8fa-4153-aa5c-498ea936e5d1.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR018930'" && ln -s '/tmp/tmprsgjhw6k/files/3/6/1/dataset_3616d219-d8fa-4153-aa5c-498ea936e5d1.dat' 'multiqc_WDir/picard_2/markdups_0/ERR018930' && grep -q 'MarkDuplicates' /tmp/tmprsgjhw6k/files/0/4/c/dataset_04c86bd6-57cc-4204-b620-2cf2e68dd790.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR1035492'" && ln -s '/tmp/tmprsgjhw6k/files/0/4/c/dataset_04c86bd6-57cc-4204-b620-2cf2e68dd790.dat' 'multiqc_WDir/picard_2/markdups_0/ERR1035492' && multiqc multiqc_WDir --filename 'report' && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "9ff130dc9a6c11efb160c573a96f40c7" ` |
| chromInfo | ` "/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comment | ` "" ` |
| dbkey | ` "?" ` |
| export | ` false ` |
| flat | ` false ` |
| results | ` [{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 8, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}] ` |
| saveLog | ` "false" ` |
| title | ` "" ` |
</details>
</details>-
Other invocation details
- **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * ccb3e58f5d9b49d5 - **history_state** * error - **invocation_id** * ccb3e58f5d9b49d5 - **invocation_state** * scheduled - **workflow_id** * ccb3e58f5d9b49d5
Hello! This is an automated update of the following workflow: workflows/variant-calling/haploid-variant-calling-wgs-pe. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.
By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6should be updated totoolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2should be updated totoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1should be updated totoolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2should be updated totoolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2should be updated totoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2should be updated totoolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0The workflow release number has been updated from 0.1 to 0.2.
If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected. Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates. To ignore manual changes and allow autoupdates, delete the branch.